Gamefreak have established that gyms use different pokemon against challengers depending on how many badges that challenger has.
So I was thinking, with all the complaints of linearity lately, maybe Gen 7 should take the LoZ: A Link Between Worlds route and make it that you can face the gyms in any order. That way you can explore all you want without being forced to fight that city's gym to progress to the next route, fans wouldn't complain about linearity, and it would feel like an adventure that could change every time you play.
It would also be good for type advantage gyms. Start with a grass starter and don't have good pokemon to face, say, a flying gym? Skip it, find pokemon later that are strong against that type, and return to the gym for a more fair fight.
Rate this idea /vp/